R Notebook

obj.mouse <- ClusterSCT(obj.mouse, c(1))
obj.m.mouse <- ClusterSCT(obj.m.mouse, c(1))
obj.opossum <- ClusterSCT(obj.opossum, c(1))
obj.m.opossum <- ClusterSCT(obj.m.opossum, c(1))

obj.mouse <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_mouse.rds")

Loading required package: SeuratObject
Loading required package: sp

obj.opossum <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_opossum.rds")
objs.i.mouse <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_i_mouse.rds")
objs.i.opossum <- readRDS("E:/Transcriptomics_V1/Integration/Opossum_Mouse-P38/obj_i_opossum.rds")

DimPlot(obj.mouse, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.mouse, reduction = "umap", group.by = "subclass", label = TRUE, repel = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.mouse, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

obj.mouse$subclass.IT <- obj.mouse$subclass
obj.mouse$subclass.IT[obj.mouse$subclass %in% c("L2/3", "L4", "L5IT", "L6IT")] <-  "IT"
p <- DimPlot(obj.mouse, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

p <- DimPlot(obj.mouse, reduction = "umap", group.by = "subclass.IT", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_SubclassIT_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_SubclassIT_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

DimPlot(obj.m.mouse, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.mouse, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.mouse, reduction = "umap", group.by = "predicted.subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.mouse, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

p <- DimPlot(obj.m.mouse, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_IntSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_Subclass_IntSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

p <- DimPlot(obj.m.mouse, reduction = "umap", group.by = "predicted.subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_PredictedSubclass_IntSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Mouse-P38_V1_All_UMAP_PredictedSubclass_IntSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

DimPlot(obj.opossum, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.opossum, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.opossum, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

obj.opossum$subclass.IT <- obj.opossum$subclass
obj.opossum$subclass.IT[obj.opossum$subclass %in% c("IT_A", "IT_B", "IT_C", "IT_D", "IT_E")] <-  "IT"
p <- DimPlot(obj.opossum, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_Subclass_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_Subclass_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

p <- DimPlot(obj.opossum, reduction = "umap", group.by = "subclass.IT", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_SubclassIT_FullSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_SubclassIT_FullSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

DimPlot(obj.m.opossum, reduction = "umap", group.by = "sample", label = FALSE, raster = FALSE, shuffle = TRUE) + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.opossum, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.opossum, reduction = "umap", group.by = "predicted.subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

DimPlot(obj.m.opossum, reduction = "umap", group.by = "type", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()

p <- DimPlot(obj.m.opossum, reduction = "umap", group.by = "subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_Subclass_IntSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_Subclass_IntSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

p <- DimPlot(obj.m.opossum, reduction = "umap", group.by = "predicted.subclass", label = TRUE, raster = FALSE, shuffle = TRUE) + NoLegend() + xlim(-18, 18) + ylim(-18, 18) + coord_equal()
ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_PredictedSubclass_IntSpace.svg", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

ggsave("E:/Opossum_Paper/Figure 1/Opossum_V1_All_UMAP_PredictedSubclass_IntSpace.png", plot = p, dpi = 300)

Saving 7.29 x 4.51 in image

PlotMapping(list(objs.m.mouse[[1]], objs.m.opossum[[1]]), ident.order = c("IT", "L2/3", "L4", "L5IT", "L6IT", "L5NP", "L5PT", "L6CT", "L6b"))

PlotMapping(list(objs.m.mouse[[2]], objs.m.opossum[[2]]), ident.order = c("Pvalb", "Sst", "Vip", "Lamp5", "Frem1", "Stac", "Meis2"))

PlotMapping(list(objs.m.mouse[[3]], objs.m.opossum[[3]]), ident.order = c("Astro", "Micro", "OD", "OPC", "Endo", "VLMC"))

Idents(objs.m.opossum[[1]]) <- "subclass"
levels(objs.m.opossum[[1]]) <- c("IT_A", "IT_B", "IT_C", "IT_D", "IT_E", "L5NP", "L5PT", "L6CT", "L6b")
VlnPlot(objs.m.opossum[[1]], "predicted.subclass.score") + NoLegend()

Idents(objs.m.opossum[[2]]) <- "subclass"
levels(objs.m.opossum[[2]]) <- c("Pvalb", "Sst", "Vip", "Lamp5", "Frem1", "Meis2")
VlnPlot(objs.m.opossum[[2]], "predicted.subclass.score") + theme(legend.spacing.x = unit(2.0, 'cm'))

Idents(objs.m.opossum[[3]]) <- "subclass"
levels(objs.m.opossum[[3]]) <- c("Astro", "Micro", "OD", "OPC", "Endo", "VLMC")
VlnPlot(objs.m.opossum[[3]], "predicted.subclass.score") + theme(legend.spacing.x = unit(2.0, 'cm'))

Idents(obj.m.opossum) <- "subclass"
levels(obj.m.opossum) <- c("IT_A", "IT_B", "IT_C", "IT_D", "IT_E", "L5NP", "L5PT", "L6CT", "L6b", 
                               "Pvalb", "Sst", "Vip", "Lamp5", "Frem1", "Meis2", 
                               "Astro", "Micro", "OD", "OPC", "Endo", "VLMC")
VlnPlot(obj.m.opossum, "predicted.subclass.score") + NoLegend()